e-BioDiv: Open Biodiversity FAIR-ification Services for Biospecimens stored in Swiss Natural History Museums

The Earth’s scholarly knowledge about species diversity (biodiversity) is  included  in  a  corpus  of  several hundred  million  pages  of  publications  spanning  over  250  years,  with  an  arbitrary  starting  point  of  1753  for plants  and  1758  for  animals.  Each  year  an  estimated  19,000  animal  and  plant  species  and  a  multiple  of augmentations  of  data  are  added  to  the  already  approximately  known  1.9M  species.  The  data  about  each species  are  included  in  highly  structured  taxonomic  treatments  and  figures.  Increasingly  these  treatments include implicit links to the data used to describe and augment it, such as omic and digitized specimen data produced by SwissBioCollection. Because of its structure, this data can be extracted automatically to a high degree,  bidirectionally  linked  from  the  literature  to  the  cited  resources  and  vice  versa,  made  FAIR,  and immediately reused by data aggregators such as GBIF and other researchers.The proposed e-BiodDiv will on the one hand provide a service for Swiss biodiversity scientists to access and disseminate their research data about species in legacy and prospective publications, provide access to data about their collections, scientists and specimens. It will complement the recently funded SwissBioCollection program and genomic data. On the other hand, importing treatments into the Swiss Institute of Bioinformatics Literature Services (SIBiLS) opens them for text and data mining through SIBiLS dedicated tools, and by the life science community.

To  a  large  extent,  this  customized  service  is  based  on  existing  services  such  as  the  Biodiversity  Literature Repository (BLR), Plazi TreatmentBank (TB), and Zenodo.The long term goal is to integrate this service in the portfolio of SIBiLS linking the biodiversity research data infrastructure in Switzerland with the -omics infrastructure. This  project  will  complement  and  make  use  of  the  Horizon  2020  funded  research  infrastructure  (BiCIKL: https://www.dissco.eu/presentation-bicikl-rda-vp17/) development  by  providing  the  specific  annotation  services  for  the  Swiss  based  scientists,  and  make  a production level import of taxonomic treatments into SIBiLS (https://candy.hesge.ch/SIBiLS/).

In addition to Patrick Ruch’s team at HES-SO and SIB (Swiss Institute of Bioinformatics, https://www.sib.swiss/patrick-ruch-group) and Beat Esterman’s team at BFH, the project is built on the direct contribution of Plazi and the Natural History Museum of Bern (NMBE). The  Swiss-based  BLR  and  TB  are the world’s leading services of liberating biodiversity data imprisoned in PDFs (portable document format) and a major contributor to the Global Biodiversity Information Facility (GBIF) where the FAIR data is reused.

Wednesday, September 1, 2021
Thursday, August 31, 2023
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